Protect Molly Hooper
by you-d0count
Summary: Molly has always been there for him and she always did everything he needed her to do. But this time he didn't need anything from her. He needs to be there for her, to protect her from Moriarty.
1. home visit

**a/n: Hey guys! So I came up with the idea of writing this story after watching His Last Vow for the 452347835 time. I am really unsure if I should keep this story as a one-shot or carry on writing more chapters so please review of what you think and if I should carry on. THANKS!**

**P.S. unfortunately I do not own Sherlock which upsets me deeply. **

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He stood outside her door as he rummaged through his pockets for her keys. He sighed heavily as he inserted the key into the door and turned it slowly. He pushed the door open silently before entering her flat. The door closed softly as he stumbled carefully into the darkness of the flat. His vision became clearer as a sliver of light came from her room as he walked closer. His hand rested on the door knob and he stood there in silence. Toby purred fondly as he walked closely around his legs. He looked down at the cat, lent down and ran his slender fingers across Toby's back. He smiled in amusement as the cat nuzzled his face into his palm. He then stood up straight and opened the bedroom door.

The face on the muted TV was the first thing that caught Sherlock's eye. The familiar face replayed on the screen over and over again. But this time it wasn't deliberate it was the news networks repeating news reports of the return of Moriarty that have been on every network for the past week and a half. He looked away from the TV with disgusted and looked over towards the bed.

His face softened as he saw the small frame of Molly Hooper lay in a bundle of blankets. He walked closer towards her and noticed she was clenching his t-shirt that he leaves here for whenever he stays. He walked over to "his" side of the bed and sat down softly next to her. He could see her begin to stir at the sudden weight change on the side of the bed. Her eyes fluttered open and Sherlock smiled down at her. She sat up in her bed as she smiled tiredly back at him.

"Sherlock, what are you doing here? Are you okay?" She said her voice half tired half concerned. Silently, Sherlock removed his t-shirt from Molly's grip, placed it on the floor and lay down beside her. Molly rested her head back down on the pillow beside Sherlock. She lies down on her side and looked at Sherlock with a worried look.

"What do you need?" She asked. She sounded exactly like she did back before the fall. When he turned to her for help in his darkest hour. But this time he didn't need anything from her. He needs to be there _for _her, to protect her. Sherlock look over to Molly and pulled her into his chest.

"Go back to sleep Molly." He said in a hushed whisper. Molly rested her head against his chest and inhaled his scent. She could hear the softness of his heart beat against her ear and drifted back into a deep sleep within minutes. Sherlock gently placed his chin on top of her head and held on to Molly close. He smiled to himself as he could hear Molly's soft breaths as she slept and before he knew it he was asleep himself, the first time in three days.

Molly woke the next morning to find that Sherlock was no longer asleep beside her. It was normal for Sherlock to disappear before Molly woke up but she hope this time he would stay. She wondered sleepily into the kitchen and stopped abruptly when she saw the slender man stood making coffee.

"Ah, good morning Miss Hooper. I have made you some coffee Lestrade called saying he needs my help at a scene in an hour and I will need your assistance." Sherlock said as he turned to face her with a bright smile on his face. He offered her some coffee and she accepted with a small smile to thank him. He then walked towards Molly's bedroom before she began to speak.

"Why did you show up at three in the morning Sherlock?" He stopped suddenly before turning around and walked back towards her.

"Because, Molly, Moriarty is back. And whatever it takes he is going to destroy and attack everyone that I love and care about. That includes you. I need to protect you, no matter what." Sherlock smiled down at Molly as she smiled back. He cupped her cheek and planted a soft kiss on the top of her head. Sherlock then strolled back towards Molly's room before shouting over his shoulder towards her. "Be ready in 30 minutes. We have a murder to solve Molly Hooper."


	2. late night messages

**HI GUYS! Thank you so much for the people that have reviewed, followed and favourite this story. I decided to continue the story! So this chapter is based a few days after the first one. I think it is really sweet and fluffy at the beginning but there is a twist near the end. Hope you enjoy! **

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_Molly? – SH _

_Molly, are you awake? – SH_

_Molly Hooper for goodness sake answer me – SH_

_I need your help with something and John sounded pretty pissed when I rang him – SH_

_If you don't answer my text I will have to ring you – SH _

_*Incoming call*_

Molly groaned as she rolled over and reached for her phone.

"What do you want Sherlock?" She answered with a drowsy voice.

"_You weren't answering any of my text messages therefore I rang you instead." _

"I didn't answer your text because I was asleep Sherlock." She said as she rolled onto her back.

"_Why? It's only three in the morning"_

"Exactly, it's three in the morning. We humans are not nocturnal like you Mr Holmes" She smiled as she could her Sherlock laugh at the other end of the phone.

"So what's so important that you need to call me at this time in the morning?"

"_Molly, what I am about to ask you is so important I need your full attention?" _Molly sat up in her bed at the seriousness in his voice.

"What's wrong?" There was a long pause before Sherlock replied.

"_What can I get Mary and John for their baby shower?" _ Molly groaned loudly as she fell back onto her pillow and clenching the bridge of her nose.

"For god sake Sherlock! What makes you think that's so important that you need to ring me up at three in the morning?"

"_It's important to me! I haven't slept in three days because I have been so busy think about what to get the baby. I may be a genius Molly but when it comes to things such as sentiment and the concept of caring for others is very daunting for me." _Molly could hear the distress in Sherlock's voice and her heart sank.

"Well the fact that you said that getting them something for the baby is important to you does show that you can care Sherlock, in your own way. I suggest that you get them something unique, something that John and Mary are going to love, something only Sherlock Holmes can give them." Molly could imagine Sherlock sat there with his thoughtful face on as he pondered over Molly's idea.

"_Molly Hooper, have I ever told you how amazingly clever you are. That is a fantastic idea, thank you." _ Molly smiled at the compliment that Sherlock just gave her.

"_Well, I will leave you to go back to sleep. Thanks again Molly. Good night" _

"Goodnight Sherlock." Molly hung up the phone and placed it back on her bedside table. Molly rolled over back onto her side and closed her eyes. She had almost fallen asleep when she heard something at the door. Her eyes instantly shot open and she jumped out of bed. She walked out of her room, grabbing the tennis racket from behind her wardrobe. She walked towards her front door to find an envelope on her door mat. She knelt down and opened it.

_**See you soon my princess **_

_**Lots of love **_

_**JM **_

_**XXXXXXXXXXXX**_

Molly froze in terror as she read the note. Blood rushed to her head and her heart pounded heavily against her chest. She dropped the piece of paper and sprinted back to her room. She slammed the door behind her and pressed her back against her door. The only sound to be heard in her flat was her heavy, unsteady breathing. Her eyes burnt with the tears that she wouldn't allow to escape. Her phone on her beside lit up. Molly hesitated for a moment before walking towards it. She gingerly picked up the phone and read the text message.

_Come to Baker Street now – SH_

_And bring an overnight bag – SH_

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**_So what do you think? I wasn't going to bring Moriarty into the equation until a few more chapters in but this idea came to me and I prefer the direction that I am going with it now compared to the one way I was originally going to do it. Hoped you liked it and please review. Thank you!_**


	3. precious pathologist

**Hi guys! I want to say a huge thanks to everyone that has followed and reviewed my story it means so much. I realised that Sherlock my be slightly out of character in this chapter but I like him being all sweet and lovely to Molly. Anyway hope you enjoy **

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Molly shivered violently as she sat in the back of the taxi heading towards Baker Street. She clutched the letter she had received and hour before in her hand tightly. Hot tears streamed down her pale cheeks. She felt like she was about to throw up everything she had eaten in the past twenty four hours. The taxi driver kept looking at her through the mirror to ensure that she was okay. The taxi came to a halt as it reached Baker Street. She sat there for a moment before plucking up the courage to get out. She handed over the money to the man sat in front of her, grabbed her over night bag and climbed out of the car. She knocked on the door softly and waited for a response. She could hear Mrs Hudson shouting Sherlock. She opened the door and pulled Molly inside.

"Oh dear, look at you. You look so shaken up. Don't worry Sherlock should-" Mrs Hudson stopped mid sentence as she heard Sherlock rush down the stairs. He pulled Molly into his arms and her timid frame relaxed into his. Molly let even more tears escape as she took in Sherlock's scent.

"I'll go make you both some tea. Go take her upstairs Sherlock dear." Mrs Hudson voiced as she walked into the kitchen of her own flat. Sherlock pulled away from Molly, still keeping her fairly close, and wiped away the tears rolling down her cheeks.

"Don't worry Molly. I will not let him come anywhere near you, understand?" Molly nodded in reply as she breathed slowly to calm herself. Sherlock snacked one of his arms around her waist and led her upstairs towards the flat, taking her bag in the process. Once they got upstairs, Sherlock took Molly's bag into his bedroom and Molly went into the living room. She threw herself on the the sofa and ran her free hand through her hair. She leant over to the coffee table and placed down the crumpled up letter in her hand. She then reached over for the only other piece of paper on the table that was exactly the same as the one she received.

**You can't protect your precious pathologist forever Sherlock **

**Like I said before I will burn the heart out of you **

**Many happy returns my dear **

**JM **

**XXXXXXXXXXXXXX**

"So this is how you knew about my letter from Jim?" Her distressed voice asked as Sherlock came into view. He walked over to her and knelt down in front of her. He took her trembling hands into his steady hands. He gently brushed his thumb over her knuckles to comfort her. He looked up to her and saw the terror in her eyes. "You should go to sleep." He said softly. Molly nodded her head slowly and laid down on the sofa. Sherlock rushed over to his room and emerged moments later with a blanket. When he reached Molly she had already fallen to sleep. He gently draped the blanket over her and lightly pressed his lips on her forehead. He let out a loud sigh and sat on the floor beside Molly. He ran his slender fingers through his hair and across his face. He then reached out and grabbed both of the letters that were on the coffee table. He quickly glanced over the two letters before throwing them back onto the table. He jumped up from where he was sitting and began pacing and mumbling things to himself. As he continued to pace he could hear Mrs Hudson's light footstep creek up the stairs. She walked into the living room and place a tray of tea onto the table. She stood up straight and looked down at Molly.

"Poor dear, she looks so helpless." She walked over to Molly and re-arranged the blanket that Sherlock had put over her. He watched Mrs Hudson as she walked back over to him. "I can't imagine someone wanting to hurt someone who's as sweet and caring as Molly." She crossed her arms and looked up at Sherlock. He placed his hand on her shoulder and looked down at her. "I'm not going to let them." His voice was low and unsteady. Mrs Hudson reached up and kissed him on the cheek. He smiled at her and she returned the gesture. "I'm going back to bed, if you need anything Sherlock don't hesitate to shout." She said as she walked back out of the door. Sherlock took out his phone and sent a message to John.

_Come over to Baker Street first as soon as you wake up – SH_

_Bring Mary – SH_

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Sherlock was woken up by muffled talking coming from the kitchen. He rolled out of bed, threw on his dressing gown and staggered towards the noise. When he reached the kitchen he saw Mary, John and Molly all sat be the table. Molly looked up at Sherlock and flashed him small smile. He walked towards the kettle and re-boiled the water before making himself a cup of coffee. He took a sip and let out a soft sigh before walking back over the his friends. "So the reason I need you here was-"

"We know, Sherlock. Molly told us." Mary said looking up at him. Sherlock moved closer to Molly and place his free hand on her shoulder.

"So was it him? Was it Moriarty that sent the letters?" John asked from the other side of the table.

"Well the hand writing from the letters is very similar from the "Get Sherlock" note that he wrote back when he stole the crown jewels. But the writer of the letters was clearly right handed and Moriarty was left handed. So the person who sent them was either one of Moriarty's handy men or a relative."

"Even if it was Moriarty, how could he have survived getting shot in the head?" Mary asked. Sherlock stayed quite for a moment he looked around to all his friends. All three of them had a hopeful look on their faces, wishing that Sherlock had the answer.

"I honestly don't know." He looked down at the floor, feeling like he had disappointed his friends. Molly reached up and placed her hand on top of his. He looked up at her and she smiled reassuringly at him. He took her hand and gently kissed it as he sat down next to her. "But my main focus right now is to ensure that you are all safe. Now, John and Mary. I defiantly think that you won't want to move back into Baker Street, especially with a baby one the way so I will ask Mycroft to increase the security around your house."

"Wait? Increase?" John asked confused.

"Well, yes. Do you think I would leave my best friend without any protection. Seriously John I thought you were smarter then that." John smiled and then frowned at the back handed compliment that Sherlock has just given him.

"What about me?" Molly said softly.

"You will have to move in here obviously."

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**I am super excited to write about Molly living with Sherlock and them being domestic and seeing their relationship develop omg! Thank you again and please do review! **

**P.S SHERLOCK ADORES MOLLY BYE **


	4. unknown feelings

** Hey guys I'm back! I want to say a HUGE thank you to everyone that has followed and reviewed this story. It means the whole world to me. SO I hope you enjoy this next chapter and please review afterwards **

**PS there is a little surprise at the end**

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The soft humming of police cars and hushed voices from outside was all Sherlock could hear as he stared at the wall in deep concentration. He stood on the sofa examining every inch of the collection of pictures, maps and newspaper articles. Newspapers and magazines with Moriarty's and his face plastered all over them littered the living room floor. Sherlock's phone gently buzzed from from the coffee table but he remained in his position. Molly emerged from the kitchen and placed two cups of coffee next to the phone.

"You want me to get that?" Molly said from behind Sherlock. Sherlock replied with a muffled yes and Molly rolled her eyes in response. She picked up the phone from the table and read the text message to herself.

"It's Greg; he says he has some information relating to Moriarty and he'll be round in half an hour." Molly said out loud. Sherlock stayed silent for a moment before turning his attention to Molly. He jumped down from the sofa and walked over to her.

"That's great." He said smiling as he reached for the phone from Molly. He sent a quick text to John and then reached down for his coffee. Molly watched him for a moment. He put the cup back onto the table and walked back to the sofa. He then went back to concentrate on the wall. He felt a sudden weight change at the side of him and looked down to see Molly mimicking the way he was standing. A small smile spread across his face as he watched Molly read and try to understand the information in front of her.

"Do you have any idea what any of this means?" Sherlock asked with a smug look on his face.

"Nope. Not a clue." She replied as she continued to concentrate on the wall. Sherlock let out a soft chuckle before placing his hand on the small of her back to and pulled her closer to explain.

"These here," he said pointing to the newspaper articles, "are every newspaper report about Moriarty from the day after my fall to last week." He moved his fingers towards some pictures and Molly's gaze followed. "These are pictures of people that have ever had contact with Moriarty and are known allies with him. If they start acting strange or do something out of the ordinary; we will know something is going on."

"Wait? Isn't that's Irene Adler? I thought she was dead?" Molly asked pointing up to the picture of the woman.

"Yeah...no, she faked her death. And then nearly died again but I helped her out of that one. It's very complicated" Sherlock said looking down at Molly who had a bemused look on her face.

"Can I ask you something?"

"Sure."

"Do all psychopaths fake their deaths?"

"Firstly, I'm a highly functioning sociopath and secondly we don't know if Moriarty is –"

"Do you have annual meetings and discuss different ways to fake your death?"

"Molly..."

"I bet you all sit there and play cluedo and drink tea."

"Molly, can I continue explaining please?" Sherlock said as Molly giggled.

"Yeah, sorry. What are the maps for? " She asked as she tried to compose herself.

"Ah, the maps! They are to show the location of everyone in London with the last name Moriarty." He said pointing up to the maps.

"Wow, that's a lot of Moriarty's. How are you going to narrow it down?" Molly asked as her eyes skimmed across the maps.

"That is where Lestrade comes in. I asked him to get me all records of people with the last name Moriarty. If he has any living relatives will find out through them." Sherlock smiled at Molly and then jumped off the sofa. He walked over to the coffee table and picked up his drink.

"So what do you think?" He asked as Molly made her way across the room.

"Brilliant." She said smiling up at him. She reached up and planted a soft kiss on his cheek.

It was just a little over a month since Molly had moved in and they have become extremely close. Molly was no longer nervous and embarrassed around him and Sherlock was more caring and affectionate towards her. But he still manages to piss Molly off. This leads to her storming off to her room. This then leads to Sherlock following an hour later with a tray of tea and Molly's favourite biscuits. And of course she couldn't stay mad at him for long.

Molly sat down in John's old chair and crossed her legs. Sherlock followed and sat opposite. They spent the next half an hour talking about things like how work was going for Molly and what they were wanting for dinner later on that night. Molly would occasionally make a comment about Sherlock's "_secret club for psychopaths that fake their deaths"_ and he would just laugh at her.

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Sherlock huffed and ruffled his hair as he threw the last report onto the table. It was four in the morning and he had just finished looking through all the records. Molly was asleep on the sofa and John and Lestrade had left about an hour ago. After looking through files for the past 9 hours they found three people that could possibly be related to Moriarty. But them three people had a very high chance of being a red herring. He just felt like giving up.

In that moment he felt vulnerable. For the first time in his career he was unable to work out what was going on and it pained him. Not because it would bruise his ego if he didn't get it right. No, it wasn't that at all. It was the fact that if he made one mistake, one error, one fault, he would be putting Molly in so much danger. The sooner he worked it out, the sooner she would be safe. He looked over at her and watched her sleep for a moment. All he wanted to do was lie next to her, hold her close and never let go.

He wasn't quite sure where the sudden affection and desperate need to be with her all the time came from. But he knew that he's feelings for her increased every moment they were together. He loved all the little things that she did. Like the way she giggled when something funny happens on the TV or the way she crinkles up her nose when she yawns. When she smiles at him, he feels a warm sensation spread through his body. She keeps him up at night, the curious case of Molly Hooper. How she was so ordinary and so extraordinary at the same time.

He wasn't ready to admit to not only to others but himself that he was in love with Molly. The moment was too risky. Them being in a serious, loving relationship at that moment could put her in even more danger.

Does he really want a serious, loving relationship with her? He had never really been in a relationship before. He went out with a girl brief in University, but that was more of a physical relationship. He had to admit he was attracted to Irene at one point when she was around. And the relationship he had with Janine wasn't real and only lasted a month. So in short he wasn't the best in relationships. He wanted Molly to be happy and he knew he couldn't make her happy.

He ran his fingers through his hair in frustration and then stood up from his desk and strode into the kitchen to make a drink to clear his head. He put on the kettle and pulled out a mug from the cupboard. He looked over at Molly and saw she was beginning to stir so he pulled another one out. Molly staggered into the kitchen sleepily and sat down at the table. She yawned as Sherlock put a cup of tea in front of her.

"So did you find anyone?" She asked as she took a sip.

"Yeah, three people. There's a Dr Moriarty that worked at London Bridge Hospital, Miss Alice Moriarty; a teacher at City of London School for Girls and a J Moriarty, who is currently unemployed. Other then all being Irish there is no other information that linked them to Jim." Sherlock said as he flopping in the kitchen chair opposite Molly. Molly studied his face and saw the defeated look in his eye. He looked tired, very, very tired. She sighed softly and reaches over the table and gripped onto his hand.

"I can have a look at the medical records at St Bart's, see if any of them have similar medical history as Jim, if they share any genetic information things like that. We can work this out Sherlock." She squeezed his hand in reassurance and Sherlock ran his thumb over her knuckle in response.

"You should get some sleep." She said as she stood from the chair. Sherlock did as well and met Molly half way around the table. Molly wrapped her arms around his neck and pulled him into a hug. Sherlock was taken back for a moment but then wrapped his arms around her waist and held her tightly.

"Everything is going to be okay." She whispered softly into Sherlock's ear. Sherlock buried his head into the crook of Molly's neck and took in her scent. He felt his heart began to race as Molly began to pull away. He didn't want it to end. He felt safe and secure in her embrace. He hesitated before he began pulling away as well.

They were face to face now. Molly still had her arms around his neck and Sherlock's arms rested perfectly around Molly's waist. Molly's breath caught in her throat as she looked deeply into Sherlock's glorious eyes. Before they both knew what they were doing their faces were centimetres away from each other. Sherlock heart at this point was nearly coming out of his chest. He swallowed and then found his courage.

He lent down and gentle pressed his lips onto Molly's. Molly hesitated but then kissed back. She wrapped her around his neck tighter and Sherlock pulled her in closer. Molly melted into Sherlock as he deepened the kiss. Her lips were soft against his and her taste was intoxicating. Molly moved her hands from the back of his neck and ran them through his thick, wild curls.

Sherlock gripped Molly tightly and hungrily moved his lips against hers. They both felt so natural as they kissed, their lips fitting together perfectly. Molly's lips began to tingle as she continued to kiss Sherlock. This kiss wasn't like any other kiss she had before. Not like a kiss with Tom. This was different. It wasn't a heat of the moment kiss, filled with passion and lust. It was a long time waited kiss, filled with love and care.

They both pulled away at the same time, gasping for air. Sherlock looked down at Molly and gently rested his forehead against hers. Molly let out a soft giggle which led to Sherlock letting out a hearty chuckle.

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***THROWS ARMS IN THE AIR AND RUNS AWAY***


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